We use the data/mammalian_REM2_codons.SA.fasta.SLAC.json file as input, it is borrowed from the AOC-REM2 analysis.
This file is parsed using the scripts/ancestralevolution.py script. Resulting in data/REM2_AA.fasta, data/REM2_DNA.fasta', and data/REM2_MSA.fasta'
We calculate TN93 genetic distances on the `data/REM2_MSA.fasta' file
A bash command is used to split the multifasta file data/REM2_DNA.fasta' into single sequence fasta files in data
/slac_asr`
We then generated PDB structures of all sequences using Colabfold's batch mode.
We extracted the Rank 1 PDB structure for each sequence
And calculated TM-Scores
Results are examined using the scripts in the notebooks folder